It used to be, if you used something like xPadder, and I'm assuming JoytoKey does the same, emulating a keypress whenever you press a controller button.
But emulated keypress detection has been removed in order to prevent cheating, so in order for it to work now, game controller buttons need to be added and supported officially. I'd like to see this as well if possible.

Yea I'd really like to see this put in at some point.
I've recently gotten the controller and I'm realizing just how many key presses and clicks are going unrecorded because WhatPulse doesn't pick them up.

I wonder if they would be able to also make it pick up the keys from games that don't need xPadder or JoytoKey to use the controller.